Sounds to me that your having a de-paraffining problem. Check your xylene or
clearing agent, maybe there is water in them or they are not as clean as they
should be. Are you on a daily rotation/change of staining/de-paraffin
reagents? Maybe, your oven isn't hot enough to melt some paraffin of
For the pale H&E, has the wax been completely removed in the xylene. If slides
are dried upright, then the wax flows down the slide possibly covering the last
section, requiring longer in the dewax solution. Secondly, after the
differentiation stage, the acid/alcohol again may be collecting at t
